multiple exons aligned to assemblies

[Lu Zheng]

Hey guys,
Recently, I want to try the mRNA-to-genomic alignment. I knew the software Spidey and Splign could do this. But these programs just only accept a single genomic sequence at a time, but not a genome fasta file containing multiple assemblies. I want to align multiple mRNA to multiple assemblies. What software can be used to do this? Thanks!

[Gig77]

Give genBlastG a try

[Lu Zheng]

Give genBlastG a try

Thank you so much! I will try.